A method for determining one or a set of optimal reagent oligonucleotide
sequences used in a biochemical method for evaluating a target nucleic
acid sequence having a target feature by defining a set of exclusion
values or ranking values specific to the biochemical method, generating
candidate reagent oligonucleotide sequences, evaluating the candidate
reagent oligonucleotide sequences against the exclusion or ranking
parameters, selecting at least one optimal reagent oligonucleotide
sequence for the selected biochemical method as applied to the target
nucleic acid sequence.